Citrus Sinensis ID: 015039

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410----
MDKGPLLLENVRNMTSQRVKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKVAKFDCGPVEGSHLGNSSSESHSPGASGSNVAVGMSDSSITALESECKNDSLEKMVNCELHGTFKSKCEYQAPDMEKCPSSHDMDRFDELDSDDNVLLSSILSKCKKRVKSTVLGTKVKRLRKPTKRYIEESSDLKPGSLMRGQNVSTATLKDKHPKVTPCNGSSKGSQVASESWLRGGRLKKRSPILGFESDDDIFSSDSDDDRVRKRKSKIDDRRKNQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFFF
cccccHHHHHHccccEEEEEEcccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccHHccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHcccccccccccHHHHHHHHHHHHHccccc
ccccHHHHHHccccccEEEEEcccccccHHHHHHHHHHHHccccccccEEccEEcccccccccccccccccccEEccccccccccccccccccccccEEEccccccccccHHHHHccccccccccccccccEcccccccccccccccccccccccccccccccccccEEEEcccccccccHHcccccHccEEEEEHcccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcc
MDKGPLLLENVRNMTSQRVKVEESFVPAFKDKAAEVSNllaepkcdhasvdgVLSFgrenlgkssgmdgfsyefefgfrtncggldsfttqgeddLKLEVLDGLlddidevddfhaandlstvcddFLLDIEFTEkvakfdcgpvegshlgnssseshspgasgsnvavgmsdsSITALESEckndslekmvncelhgtfkskceyqapdmekcpsshdmdrfdeldsddNVLLSSILSKCKKRvkstvlgtkvkrlrkptkryieessdlkpgslmrgqnvstatlkdkhpkvtpcngsskgsqvaseswlrggrlkkrspilgfesdddifssdsdddrVRKRKSKIDDRRKNQRMWTLSEVMKLIDGisqfgvgkwtDIKRLLfsssshrtpidLRVFFIFLYLIEQLFFF
mdkgplllenvrnmtsqrvkveesFVPAFKDKAAEVSNLlaepkcdhASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKVAKFDCGPVEGSHLgnssseshspgASGSNVAVGMSDSSITALESECKNDSLEKMVNCELHGTFKSKCEYQAPDMEKCPSSHDMDRFDELDSDDNVLLSSilskckkrvkstvlgtkvkrlrkptkryieessdlkpgslmrgQNVStatlkdkhpkvtpcngsskgsqvaseswlrggrlkkrspilgfesdddifssdsdddrvrkrkskiddrrknqrmwtlsEVMKLIDGISQFGVGKWTDIKRLLFsssshrtpidLRVFFIFLYLIEQLFFF
MDKGPLLLENVRNMTSQRVKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKlevldgllddidevddFHAANDLSTVCDDFLLDIEFTEKVAKFDCGPVegshlgnssseshspgasgsnVAVGMSDSSITALESECKNDSLEKMVNCELHGTFKSKCEYQAPDMEKCPSSHDMDRFDELDSDDNVLLSSILSKCKKRVKSTVLGTKVKRLRKPTKRYIEESSDLKPGSLMRGQNVSTATLKDKHPKVTPCNGSSKGSQVASESWLRGGRLKKRSPILGFEsdddifssdsdddrvrkrkskiddrrkNQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFFF
***********************************VSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKVAKFDCGP***********************************************VNCELHGTF*******************************VLLSSILSKCKKRVKSTVLG**********************************************************************************************************MWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFF*
******************VKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGF*******************LEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKV**********************************SDSS****************************************************************************************************************************************************************************************TLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFFF
MDKGPLLLENVRNMTSQRVKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKVAKFDCGPVEGS***********************SDSSITALESECKNDSLEKMVNCELHGTFKSKCEYQAPDMEKCPSSHDMDRFDELDSDDNVLLSSILSKCKKRVKSTVLGTKVKRLRKPTKRYIEESSDLKPGSLMRGQNVSTATLKDK**********************RGGRLKKRSPILGFESDDDIFS******************RKNQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFFF
****PLLLENVRNMTSQRVKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKVAKFDCGPVEGSHLGNS****H*PGASGSNVAVGMSDSSITALESECKNDSLEKMVNCELHGTFKSKCEYQAPDMEKCPSSHDMDRFDELDSDDNVLLSSILSKC*****************K*************************************************************************************************RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFFF
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MDKGPLLLENVRNMTSQRVKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGMDGFSYEFEFGFRTNCGGLDSFTTQGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDDFLLDIEFTEKVAKFDCGPVEGSHLGNSSSESHSPGASGSNVAVGMSDSSITALESECKNDSLEKMVNCELHGTFKSKCEYQAPDMEKCPSSHDMDRFDELDSDDNVLLSSILSKCKKRVKSTVLGTKVKRLRKPTKRYIEESSDLKPGSLMRGQNVSTATLKDKHPKVTPCNGSSKGSQVASESWLRGGRLKKRSPILGFESDDDIFSSDSDDDRVRKRKSKIDDRRKNQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQLFFF
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query414 2.2.26 [Sep-21-2011]
Q9FFY9640 Telomere repeat-binding p no no 0.176 0.114 0.294 6e-05
Q6R0E3630 Telomere repeat-binding p no no 0.137 0.090 0.333 0.0007
Q9M347400 Telomere repeat-binding p no no 0.115 0.12 0.375 0.0007
Q9C7B1619 Telomere repeat-binding p no no 0.115 0.077 0.333 0.0009
>sp|Q9FFY9|TRP4_ARATH Telomere repeat-binding protein 4 OS=Arabidopsis thaliana GN=TRP4 PE=1 SV=1 Back     alignment and function desciption
 Score = 49.3 bits (116), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 5/78 (6%)

Query: 322 PILGFESDDDIFSSDSDDDRVRKRKSKIDDRRKNQRMWTLSEVMKLIDGISQFGVGKWTD 381
           P+L  ESD       ++    + +++++  RR  +R ++++EV  L+  + + G G+W D
Sbjct: 506 PVLALESDALALVPVNE----KPKRTELSQRR-TRRPFSVTEVEALVSAVEEVGTGRWRD 560

Query: 382 IKRLLFSSSSHRTPIDLR 399
           +K   F ++SHRT +DL+
Sbjct: 561 VKLRSFENASHRTYVDLK 578
Binds specifically to the plant telomeric double-stranded DNA sequences 5'-TTTAGGG-3'. At least 2 repeats of telomeric sequences are required for binding. Induces DNA bending.
Arabidopsis thaliana (taxid: 3702)
>sp|Q6R0E3|TRP5_ARATH Telomere repeat-binding protein 5 OS=Arabidopsis thaliana GN=TRP5 PE=1 SV=2 Back     alignment and function description
>sp|Q9M347|TRP6_ARATH Telomere repeat-binding protein 6 OS=Arabidopsis thaliana GN=TRP6 PE=1 SV=1 Back     alignment and function description
>sp|Q9C7B1|TRP3_ARATH Telomere repeat-binding protein 3 OS=Arabidopsis thaliana GN=TRP3 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query414
297741622 542 unnamed protein product [Vitis vinifera] 0.932 0.712 0.446 4e-80
225440021455 PREDICTED: uncharacterized protein LOC10 0.722 0.657 0.431 6e-58
255556964 542 hypothetical protein RCOM_1355420 [Ricin 0.719 0.549 0.498 1e-55
357440365463 hypothetical protein MTR_1g063940 [Medic 0.855 0.764 0.382 2e-51
356548325477 PREDICTED: uncharacterized protein LOC10 0.850 0.737 0.397 4e-50
356533240464 PREDICTED: uncharacterized protein LOC10 0.838 0.747 0.387 1e-45
297823525395 hypothetical protein ARALYDRAFT_482686 [ 0.724 0.759 0.338 1e-41
449451024477 PREDICTED: uncharacterized protein LOC10 0.893 0.775 0.344 2e-41
449482457477 PREDICTED: uncharacterized LOC101219571 0.893 0.775 0.339 4e-41
30687001410 protein TRF-like 8 [Arabidopsis thaliana 0.734 0.741 0.330 9e-39
>gi|297741622|emb|CBI32754.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  304 bits (779), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 202/452 (44%), Positives = 268/452 (59%), Gaps = 66/452 (14%)

Query: 8   LENVRNMTSQRVKVEESFVPAFKDKAAEVSNLLAEPKCDHASVDGVLSFGRENLGKSSGM 67
           L+   NM  QRV  +ESFVPA +D+A EV +LLAEPK D+ SVDGVLS     L K   +
Sbjct: 8   LKKYVNMKCQRVNEDESFVPALEDEAIEVEHLLAEPKNDNVSVDGVLS-----LKKCLDI 62

Query: 68  DGFSYEFEFGFRTNCGGLDSFTT-QGEDDLKLEVLDGLLDDIDEVDDFHAANDLSTVCDD 126
           +     FE G  ++ GG+DS TT +GED+LKL V DG+L ++ EV D HA N LS  C+D
Sbjct: 63  EDIPGRFECGLESHSGGMDSNTTREGEDELKLGVFDGMLHEVAEVGDLHATNSLSGACED 122

Query: 127 FLLDIEFTEKVAKFDCGPVEGSHLGNSSSESHSPGASGS-NVAVGMSDSSITALE-SECK 184
           +LLDIEF E V++ D GP  GSHLGNSSSESHSPG SGS N AVG+S+SS   +   EC 
Sbjct: 123 YLLDIEFAETVSELDNGPCAGSHLGNSSSESHSPGFSGSDNGAVGISESSTGTIPVPECG 182

Query: 185 NDSLEKMVNCELHGTFKSKCEYQA---PDME-KCPSSHDMDRFDELDSDDNVLLSSILSK 240
           N+ L+KM  C LHGT +SKCE +      ME +  +S ++   D +D+  N++    L +
Sbjct: 183 NN-LDKMTICTLHGTSRSKCECKMLVEGKMELQGSASFNLQNPDGVDNVSNLVSGIPLVE 241

Query: 241 CKKRV--------KSTVLGTKV---------------------------KRLRKPTKRYI 265
            +K V        K++ +G  +                           KR+R+PT+RYI
Sbjct: 242 NRKDVTFTNLQYNKASSIGQGMKKESFAGRKGSRKRSVEASDVGMLLSEKRMRRPTRRYI 301

Query: 266 EESSDLKPGS-LMRGQNVSTAT----LKDKHPKVTPCNGSSKGSQVASESWLRG------ 314
           EE SDLK  S   R +N +T T    L ++H   T   G S    V S S+ R       
Sbjct: 302 EEFSDLKSKSNRGRPKNSTTTTKNKLLGNRHRSETHHKGFSAAPLVPSGSYGRSSDRTPF 361

Query: 315 ------GRLKKRSPILGFESDDDIFSSDSDDDRVR-KRKSKIDDRRKNQRMWTLSEVMKL 367
                 G LKK + I   +SD++   ++S+DD +  KR     DRRK+QR+WTLSEVMKL
Sbjct: 362 EVGVQKGCLKKYASISDLDSDEESSPAESEDDCMTIKRPETSGDRRKHQRLWTLSEVMKL 421

Query: 368 IDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           +DG+S +GVG+WTDIKRLLFSSS++RTP+DLR
Sbjct: 422 VDGVSHYGVGRWTDIKRLLFSSSAYRTPVDLR 453

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225440021|ref|XP_002276488.1| PREDICTED: uncharacterized protein LOC100263609 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255556964|ref|XP_002519515.1| hypothetical protein RCOM_1355420 [Ricinus communis] gi|223541378|gb|EEF42929.1| hypothetical protein RCOM_1355420 [Ricinus communis] Back     alignment and taxonomy information
>gi|357440365|ref|XP_003590460.1| hypothetical protein MTR_1g063940 [Medicago truncatula] gi|355479508|gb|AES60711.1| hypothetical protein MTR_1g063940 [Medicago truncatula] Back     alignment and taxonomy information
>gi|356548325|ref|XP_003542553.1| PREDICTED: uncharacterized protein LOC100810255 [Glycine max] Back     alignment and taxonomy information
>gi|356533240|ref|XP_003535174.1| PREDICTED: uncharacterized protein LOC100777720 [Glycine max] Back     alignment and taxonomy information
>gi|297823525|ref|XP_002879645.1| hypothetical protein ARALYDRAFT_482686 [Arabidopsis lyrata subsp. lyrata] gi|297325484|gb|EFH55904.1| hypothetical protein ARALYDRAFT_482686 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449451024|ref|XP_004143262.1| PREDICTED: uncharacterized protein LOC101219571 [Cucumis sativus] Back     alignment and taxonomy information
>gi|449482457|ref|XP_004156288.1| PREDICTED: uncharacterized LOC101219571 [Cucumis sativus] Back     alignment and taxonomy information
>gi|30687001|ref|NP_850275.1| protein TRF-like 8 [Arabidopsis thaliana] gi|79324500|ref|NP_001031497.1| protein TRF-like 8 [Arabidopsis thaliana] gi|330254243|gb|AEC09337.1| protein TRF-like 8 [Arabidopsis thaliana] gi|330254244|gb|AEC09338.1| protein TRF-like 8 [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query414
TAIR|locus:504955960410 TRFL8 "TRF-like 8" [Arabidopsi 0.108 0.109 0.666 1.4e-21
TAIR|locus:2030255630 TRFL6 "TRF-like 6" [Arabidopsi 0.108 0.071 0.555 9.7e-11
TAIR|locus:504955960 TRFL8 "TRF-like 8" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 173 (66.0 bits), Expect = 1.4e-21, Sum P(2) = 1.4e-21
 Identities = 30/45 (66%), Positives = 36/45 (80%)

Query:   355 NQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
             NQR+WTL EVM L+DGIS FGVGKWTDIK   F  ++HR P+D+R
Sbjct:   291 NQRIWTLDEVMNLVDGISHFGVGKWTDIKNHFFHYAAHRKPVDIR 335
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
TAIR|locus:2030255 TRFL6 "TRF-like 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query414
cd1166050 cd11660, SANT_TRF, Telomere repeat binding factor- 3e-11
cd0016745 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA- 2e-04
smart0071749 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII 3e-04
>gnl|CDD|212558 cd11660, SANT_TRF, Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family Back     alignment and domain information 
 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 357 RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           R WT  E   L++G+ ++GVG W  I +  +   ++RT +DL+
Sbjct: 1   RKWTDEEDEALVEGVEKYGVGNWAKILK-DYFFVNNRTSVDLK 42

Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1. Length = 50
>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains Back     alignment and domain information
>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 414
PF0024948 Myb_DNA-binding: Myb-like DNA-binding domain; Inte 98.9
smart0071749 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi 98.61
cd0016745 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do 98.47
PF1392160 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 98.06
PLN03212 249 Transcription repressor MYB5; Provisional 97.87
PLN03091 459 hypothetical protein; Provisional 97.65
TIGR0155757 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c 97.53
PLN03212 249 Transcription repressor MYB5; Provisional 97.36
PLN03091 459 hypothetical protein; Provisional 97.07
KOG0457 438 consensus Histone acetyltransferase complex SAGA/A 96.52
PF1383790 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; 96.43
KOG0048 238 consensus Transcription factor, Myb superfamily [T 96.3
PF1387378 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain 95.88
KOG0048 238 consensus Transcription factor, Myb superfamily [T 94.41
PF13325199 MCRS_N: N-terminal region of micro-spherule protei 93.64
KOG0049 939 consensus Transcription factor, Myb superfamily [T 92.67
KOG0051 607 consensus RNA polymerase I termination factor, Myb 92.49
PF09111118 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain 92.38
KOG0049 939 consensus Transcription factor, Myb superfamily [T 92.08
COG5114 432 Histone acetyltransferase complex SAGA/ADA, subuni 91.39
KOG4282 345 consensus Transcription factor GT-2 and related pr 88.45
PLN031421033 Probable chromatin-remodeling complex ATPase chain 86.42
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins Back     alignment and domain information 
Probab=98.90  E-value=8.4e-10  Score=79.76  Aligned_cols=48  Identities=25%  Similarity=0.459  Sum_probs=42.5

Q ss_pred             CCCCCHHHHHHHHHHHHhhCCCchHhhHhhhCCCCCCCCCCccchhhhhhh
Q 015039          356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLY  406 (414)
Q Consensus       356 rr~WT~eEveaLv~GV~kyGvG~Wt~Il~~~F~~f~~RT~VDLKDKWRNL~  406 (414)
                      +.+||.+|.+.|+++|++||.++|..|...+.   ..||..+++.+|++++
T Consensus         1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~---~~Rt~~qc~~~~~~~~   48 (48)
T PF00249_consen    1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMP---GGRTAKQCRSRYQNLL   48 (48)
T ss_dssp             S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHS---SSSTHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcC---CCCCHHHHHHHHHhhC
Confidence            35899999999999999999999999999887   3799999999999974

These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains Back     alignment and domain information
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains Back     alignment and domain information
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A Back     alignment and domain information
>PLN03212 Transcription repressor MYB5; Provisional Back     alignment and domain information
>PLN03091 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class Back     alignment and domain information
>PLN03212 Transcription repressor MYB5; Provisional Back     alignment and domain information
>PLN03091 hypothetical protein; Provisional Back     alignment and domain information
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics] Back     alignment and domain information
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A Back     alignment and domain information
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain Back     alignment and domain information
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>PF13325 MCRS_N: N-terminal region of micro-spherule protein Back     alignment and domain information
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription] Back     alignment and domain information
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices Back     alignment and domain information
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics] Back     alignment and domain information
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription] Back     alignment and domain information
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query414
2qhb_A86 Crystal Structure Of Ngtrf Complexed With Telomeric 3e-04
2juh_A121 Solution Structure Of Dna Binding Domain Of Ngtrf1 3e-04
2ckx_A83 Crystal Structure Of Ngtrf1, Double-Stranded Telome 3e-04
2aje_A105 Solution Structure Of The Arabidopsis Thaliana Telo 4e-04
2roh_A122 The Dna Binding Domain Of Rtbp1 Length = 122 6e-04
>pdb|2QHB|A Chain A, Crystal Structure Of Ngtrf Complexed With Telomeric Dna Length = 86 Back     alignment and structure 
Iteration: 1

 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 29/44 (65%)
Query: 356 QRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           +R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+
Sbjct: 4   RRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLK 47
>pdb|2JUH|A Chain A, Solution Structure Of Dna Binding Domain Of Ngtrf1 Length = 121 Back     alignment and structure
>pdb|2CKX|A Chain A, Crystal Structure Of Ngtrf1, Double-Stranded Telomeric Repeat Binding Factor From Nicotiana Tabacum Length = 83 Back     alignment and structure
>pdb|2AJE|A Chain A, Solution Structure Of The Arabidopsis Thaliana Telomeric Repeat-Binding Protein Dna Binding Domain Length = 105 Back     alignment and structure
>pdb|2ROH|A Chain A, The Dna Binding Domain Of Rtbp1 Length = 122 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query414
2roh_A122 RTBP1, telomere binding protein-1; plant, nucleus, 5e-16
2juh_A121 Telomere binding protein TBP1; helix, nucleus, nuc 2e-15
2ckx_A83 NGTRF1, telomere binding protein TBP1; nuclear pro 6e-15
2aje_A105 Telomere repeat-binding protein; DNA-binding, Trp, 1e-14
1vf9_A64 Telomeric repeat binding factor 2; MYB, helix-turn 3e-09
1ity_A69 TRF1; helix-turn-helix, telomeres, DNA binding, MY 3e-09
1w0u_A55 Telomeric repeat binding factor 2; telomere, DNA-b 1e-08
1w0t_A53 Telomeric repeat binding factor 1; telomere, DNA-b 2e-08
2elk_A58 SPCC24B10.08C protein; hypothetical protein, struc 2e-06
1x41_A60 Transcriptional adaptor 2-like, isoform B; transcr 2e-04
>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa} Length = 122 Back     alignment and structure
 Score = 72.9 bits (178), Expect = 5e-16
 Identities = 18/58 (31%), Positives = 34/58 (58%)

Query: 342 VRKRKSKIDDRRKNQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           + + K     +R+ +R +T++EV  L++ +   G G+W D+K   F +  HRT +DL+
Sbjct: 17  LSRSKRPDFGQRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLK 74
>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa} Length = 121 Back     alignment and structure
>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A Length = 83 Back     alignment and structure
>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3 Length = 105 Back     alignment and structure
>1vf9_A Telomeric repeat binding factor 2; MYB, helix-turn-helix, telomere, DNA binding protein; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1xg1_A 1vfc_A Length = 64 Back     alignment and structure
>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A Length = 69 Back     alignment and structure
>1w0u_A Telomeric repeat binding factor 2; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle, nuclear protein; 1.8A {Homo sapiens} SCOP: a.4.1.4 Length = 55 Back     alignment and structure
>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A Length = 53 Back     alignment and structure
>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe} Length = 58 Back     alignment and structure
>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 60 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query414
2roh_A122 RTBP1, telomere binding protein-1; plant, nucleus, 99.77
2aje_A105 Telomere repeat-binding protein; DNA-binding, Trp, 99.75
2juh_A121 Telomere binding protein TBP1; helix, nucleus, nuc 99.74
1x58_A62 Hypothetical protein 4930532D21RIK; MUS musculus a 99.73
2ckx_A83 NGTRF1, telomere binding protein TBP1; nuclear pro 99.7
3sjm_A64 Telomeric repeat-binding factor 2; human telomeric 99.5
1ity_A69 TRF1; helix-turn-helix, telomeres, DNA binding, MY 99.39
1w0t_A53 Telomeric repeat binding factor 1; telomere, DNA-b 99.37
1guu_A52 C-MYB, MYB proto-oncogene protein; transcription, 98.88
2d9a_A60 B-MYB, MYB-related protein B; DNA binding, structu 98.85
1gvd_A52 MYB proto-oncogene protein; transcription, transcr 98.76
1x41_A60 Transcriptional adaptor 2-like, isoform B; transcr 98.69
2dim_A70 Cell division cycle 5-like protein; MYB_DNA-bindin 98.65
2elk_A58 SPCC24B10.08C protein; hypothetical protein, struc 98.65
2yus_A79 SWI/SNF-related matrix-associated actin- dependent 98.63
2cu7_A72 KIAA1915 protein; nuclear protein, SANT domain, DN 98.44
2din_A66 Cell division cycle 5-like protein; MYB_DNA-bindin 98.35
2yum_A75 ZZZ3 protein, zinc finger ZZ-type-containing prote 98.33
2llk_A73 Cyclin-D-binding MYB-like transcription factor 1; 98.31
1gv2_A105 C-MYB, MYB proto-oncogene protein; transcription, 98.26
2cqr_A73 RSGI RUH-043, DNAJ homolog subfamily C member 1; m 98.21
3osg_A126 MYB21; transcription-DNA complex, MYB2, R2R3 domai 98.2
3osg_A126 MYB21; transcription-DNA complex, MYB2, R2R3 domai 98.2
1h8a_C128 AMV V-MYB, MYB transforming protein; transcription 98.18
2k9n_A107 MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind 98.17
1gv2_A105 C-MYB, MYB proto-oncogene protein; transcription, 98.16
2k9n_A107 MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind 98.13
1h8a_C128 AMV V-MYB, MYB transforming protein; transcription 98.05
3zqc_A131 MYB3; transcription-DNA complex, DNA-binding prote 98.02
3zqc_A131 MYB3; transcription-DNA complex, DNA-binding prote 98.01
2ltp_A89 Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s 97.19
1h89_C159 C-MYB, MYB proto-oncogene protein; transcription/D 97.85
1h89_C159 C-MYB, MYB proto-oncogene protein; transcription/D 97.78
2eqr_A61 N-COR1, N-COR, nuclear receptor corepressor 1; SAN 97.51
2cjj_A93 Radialis; plant development, DNA-binding protein, 97.5
3hm5_A93 DNA methyltransferase 1-associated protein 1; DNA 97.25
2cqq_A72 RSGI RUH-037, DNAJ homolog subfamily C member 1; m 97.2
1ign_A 246 Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, 97.15
4b4c_A211 Chromodomain-helicase-DNA-binding protein 1; chrom 97.11
2ebi_A86 DNA binding protein GT-1; DNA-binding domain, phos 96.58
2xb0_X270 Chromo domain-containing protein 1; hydrolase, DNA 96.36
2iw5_B235 Protein corest, REST corepressor 1; oxidoreductase 96.28
2yqk_A63 Arginine-glutamic acid dipeptide repeats protein; 96.1
4iej_A93 DNA methyltransferase 1-associated protein 1; DNA 95.88
2crg_A70 Metastasis associated protein MTA3; transcription 95.71
1wgx_A73 KIAA1903 protein; MYB DNA-binding domain, human cD 95.64
4b4c_A 211 Chromodomain-helicase-DNA-binding protein 1; chrom 94.87
1irz_A64 ARR10-B; helix-turn-helix, DNA binding protein; NM 93.32
1ofc_X304 ISWI protein; nuclear protein, chromatin remodelin 93.26
2xag_B482 REST corepressor 1; amine oxidase, chromatin regul 93.09
2y9y_A374 Imitation switch protein 1 (DEL_ATPase); transcrip 91.69
4a69_C94 Nuclear receptor corepressor 2; transcription, hyd 91.0
1fex_A59 TRF2-interacting telomeric RAP1 protein; helix tur 90.2
4eef_G74 F-HB80.4, designed hemagglutinin binding protein; 87.83
2xb0_X 270 Chromo domain-containing protein 1; hydrolase, DNA 87.36
>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa} Back     alignment and structure
Probab=99.77  E-value=2.1e-19  Score=154.68  Aligned_cols=62  Identities=29%  Similarity=0.520  Sum_probs=57.1

Q ss_pred             ccccCCCCCCCHHHHHHHHHHHHhhCCCchHhhHhhhCCCCCCCCCCccchhhhhhhhhccc
Q 015039          350 DDRRKNQRMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIEQL  411 (414)
Q Consensus       350 ~~rRK~rr~WT~eEveaLv~GV~kyGvG~Wt~Il~~~F~~f~~RT~VDLKDKWRNL~K~~~~  411 (414)
                      ..+||++++||.||+++|++||++||.|+|+.|++.+|..|.+||+||||||||||+|+..+
T Consensus        25 ~~~rr~r~~WT~EEd~~L~~gV~k~G~g~W~~I~~~~~~~~~~RT~vdlKdRWrnllk~~~~   86 (122)
T 2roh_A           25 FGQRRIRRPFTVAEVELLVEAVEHLGTGRWRDVKFRAFENVHHRTYVDLKDKWKTLVHTASI   86 (122)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHHSSSCHHHHHHHHHSSSCCCCHHHHHHHHHHHHHHHHS
T ss_pred             cCCCCCCCCCCHHHHHHHHHHHHHHCCCChHHHHHHhccccCCCCHHHHHHHHHHHHhhccC
Confidence            46788889999999999999999999999999999988778899999999999999987654
>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3 Back     alignment and structure
>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa} Back     alignment and structure
>1x58_A Hypothetical protein 4930532D21RIK; MUS musculus adult MALE testis cDNA, riken FULL-length enriched library, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A Back     alignment and structure
>3sjm_A Telomeric repeat-binding factor 2; human telomeric repeat binding protein 2, telomere, telomeri homeodomain proteins amino acid sequence; HET: DNA; 1.35A {Homo sapiens} PDB: 1xg1_A 1vfc_A 1vf9_A 1w0u_A Back     alignment and structure
>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A Back     alignment and structure
>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A Back     alignment and structure
>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A Back     alignment and structure
>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A Back     alignment and structure
>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe} Back     alignment and structure
>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens} Back     alignment and structure
>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>2din_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens} Back     alignment and structure
>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A Back     alignment and structure
>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A Back     alignment and structure
>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A Back     alignment and structure
>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3 Back     alignment and structure
>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A Back     alignment and structure
>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A Back     alignment and structure
>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A Back     alignment and structure
>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3 Back     alignment and structure
>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis} Back     alignment and structure
>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis} Back     alignment and structure
>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens} Back     alignment and structure
>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C Back     alignment and structure
>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C Back     alignment and structure
>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3 Back     alignment and structure
>3hm5_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin, structural genomics consortium, SGC, activator, chromatin regulator; HET: DNA; 1.80A {Homo sapiens} Back     alignment and structure
>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A Back     alignment and structure
>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens} Back     alignment and structure
>2ebi_A DNA binding protein GT-1; DNA-binding domain, phosphorylation; HET: DNA; NMR {Arabidopsis thaliana} PDB: 2jmw_A* Back     alignment and structure
>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A Back     alignment and structure
>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B* Back     alignment and structure
>2yqk_A Arginine-glutamic acid dipeptide repeats protein; structure genomics, SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>4iej_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin regulator, repressor, structural joint center for structural genomics; HET: DNA; 1.45A {Homo sapiens} PDB: 3hm5_A* Back     alignment and structure
>2crg_A Metastasis associated protein MTA3; transcription factor, helix turn helix, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.3 Back     alignment and structure
>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens} Back     alignment and structure
>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11 Back     alignment and structure
>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A Back     alignment and structure
>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B* Back     alignment and structure
>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A Back     alignment and structure
>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A Back     alignment and structure
>1fex_A TRF2-interacting telomeric RAP1 protein; helix turn helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Synthetic} SCOP: a.4.1.3 Back     alignment and structure
>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin, fusion of virus membrane with membrane, membrane fusion, sialic acid, virion; HET: NAG BMA; 2.70A {Artificial gene} Back     alignment and structure
>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 414
d2ckxa183 a.4.1.3 (A:578-660) Telomere binding protein TBP1 2e-06
d1w0ta_52 a.4.1.4 (A:) DNA-binding domain of human telomeric 2e-04
>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Length = 83 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Telomere binding protein TBP1
species: Tobacco (Nicotiana tabacum) [TaxId: 4097]

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 15/43 (34%), Positives = 28/43 (65%)

Query: 357 RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLR 399
           R ++++EV  L++ +   G G+W D+K   F ++ HRT +DL+
Sbjct: 1   RPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLK 43
>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 52 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query414
d2ckxa183 Telomere binding protein TBP1 {Tobacco (Nicotiana 99.59
d1w0ua_55 Telomeric repeat binding factor 2, TRF2 {Human (Ho 99.57
d1w0ta_52 DNA-binding domain of human telomeric protein, hTR 99.56
d1guua_50 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 98.82
d1gvda_52 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 98.74
d1gv2a247 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 98.53
d1x41a147 Transcriptional adaptor 2-like, TADA2L, isoform b 98.44
d1x58a149 Hypothetical protein 4930532d21rik {Mouse (Mus mus 98.43
d2cqra160 DnaJ homolog subfamily C member 1 {Human (Homo sap 98.35
d2cu7a165 MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960 98.31
d2cjja163 Radialis {Garden snapdragon (Antirrhinum majus) [T 98.11
d1xc5a168 Nuclear receptor corepressor 2 {Human (Homo sapien 98.05
d2iw5b165 REST corepressor 1, CoREST {Human (Homo sapiens) [ 98.0
d1igna186 DNA-binding domain of rap1 {Baker's yeast (Sacchar 97.69
d1irza_64 Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId 97.0
d2crga157 Metastasis associated protein MTA3 {Mouse (Mus mus 96.73
d1ug2a_95 2610100b20rik gene product {Mouse (Mus musculus) [ 95.49
d2cqqa159 DnaJ homolog subfamily C member 1 {Human (Homo sap 92.81
d1ofcx2128 SLIDE domain of the nucleosome remodeling ATPase I 89.46
>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Telomere binding protein TBP1
species: Tobacco (Nicotiana tabacum) [TaxId: 4097]

Probab=99.59  E-value=2.6e-16  Score=123.77  Aligned_cols=53  Identities=30%  Similarity=0.602  Sum_probs=49.6

Q ss_pred             CCCCHHHHHHHHHHHHhhCCCchHhhHhhhCCCCCCCCCCccchhhhhhhhhc
Q 015039          357 RMWTLSEVMKLIDGISQFGVGKWTDIKRLLFSSSSHRTPIDLRVFFIFLYLIE  409 (414)
Q Consensus       357 r~WT~eEveaLv~GV~kyGvG~Wt~Il~~~F~~f~~RT~VDLKDKWRNL~K~~  409 (414)
                      |+||.||.++|++||++||.|+|+.|.+.+|..+.+||++|+|||||||++..
T Consensus         1 r~WT~eEd~~L~~~V~~~G~~~W~~I~~~~~~~~~~Rt~~qck~RWrn~l~~~   53 (83)
T d2ckxa1           1 RPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTA   53 (83)
T ss_dssp             CCCCHHHHHHHHHHHHHHCSSCHHHHHHHHCTTCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCcccHHHHHHHHHhhccCCCHHHHHHHHHHHhhhh
Confidence            68999999999999999999999999998877778999999999999999764
>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x58a1 a.4.1.1 (A:8-56) Hypothetical protein 4930532d21rik {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]} Back     information, alignment and structure
>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ug2a_ a.4.1.3 (A:) 2610100b20rik gene product {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ofcx2 a.4.1.13 (X:851-978) SLIDE domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure